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- PDB-8vsy: Bile salt hydrolase from Arthrobacter citreus with covalent inhib... -

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Basic information

Entry
Database: PDB / ID: 8vsy
TitleBile salt hydrolase from Arthrobacter citreus with covalent inhibitor AAA-10 bound
ComponentsBile salt hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor bound / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyChem-WSR
Function and homology information
Biological speciesArthrobacter citreus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDhindwal, P. / Ruzzini, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and functional analysis of a bile salt hydrolase from the bison microbiome.
Authors: Asar, R. / Dhindwal, P. / Ruzzini, A.
History
DepositionJan 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile salt hydrolase
B: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,11514
Polymers70,6442
Non-polymers1,47112
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-60 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.760, 43.840, 87.160
Angle α, β, γ (deg.)90.00, 111.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-786-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bile salt hydrolase


Mass: 35322.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter citreus (bacteria) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 782 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-WSR / (1R,3aS,3bR,5aR,7R,9aS,9bS,11aR)-1-[(2R)-6-fluoro-5-oxohexan-2-yl]-9a,11a-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-7-yl hydrogen sulfate (non-preferred name)


Mass: 472.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H41FO5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES, 21% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.6→48.41 Å / Num. obs: 77222 / % possible obs: 98.22 % / Redundancy: 6.9 % / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 16.5
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 7571 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.95 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1567 3896 2.59 %
Rwork0.1363 --
obs0.1369 77222 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 92 770 5752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.177
X-RAY DIFFRACTIONf_dihedral_angle_d7.906765
X-RAY DIFFRACTIONf_chiral_restr0.081796
X-RAY DIFFRACTIONf_plane_restr0.011962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.23761370.19515247X-RAY DIFFRACTION97
1.62-1.640.27361370.18915166X-RAY DIFFRACTION97
1.64-1.660.21931370.17625146X-RAY DIFFRACTION97
1.66-1.680.20571400.16915229X-RAY DIFFRACTION98
1.68-1.710.20731350.16835117X-RAY DIFFRACTION97
1.71-1.730.19891400.15615247X-RAY DIFFRACTION98
1.73-1.760.17521410.15495166X-RAY DIFFRACTION98
1.76-1.790.2031350.15375144X-RAY DIFFRACTION98
1.79-1.820.181410.14825251X-RAY DIFFRACTION98
1.82-1.850.16831380.14135212X-RAY DIFFRACTION98
1.85-1.890.1721410.14485228X-RAY DIFFRACTION98
1.89-1.930.17571380.14075250X-RAY DIFFRACTION98
1.93-1.970.14071375244X-RAY DIFFRACTION98
1.97-2.020.16491400.13485214X-RAY DIFFRACTION98
2.02-2.070.15071400.13015255X-RAY DIFFRACTION98
2.07-2.120.15831420.12585273X-RAY DIFFRACTION99
2.12-2.180.15191380.13135210X-RAY DIFFRACTION99
2.18-2.260.15611430.13065244X-RAY DIFFRACTION99
2.26-2.340.12911435279X-RAY DIFFRACTION99
2.34-2.430.16251390.13515310X-RAY DIFFRACTION99
2.43-2.540.16641370.14135217X-RAY DIFFRACTION99
2.54-2.670.19131370.13625257X-RAY DIFFRACTION99
2.67-2.840.15661400.14265294X-RAY DIFFRACTION99
2.84-3.060.15351410.13555299X-RAY DIFFRACTION99
3.06-3.370.15211440.12425313X-RAY DIFFRACTION99
3.37-3.860.1161380.11035251X-RAY DIFFRACTION99
3.86-4.860.11881370.11125322X-RAY DIFFRACTION99
4.86-42.950.14641405260X-RAY DIFFRACTION99

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